We are looking for software or a web service that we can put in pictures we took using our weather balloon to create a single image, that we can use as a layer for our GIS project. Preferably free, or free for education.

3 Answers
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The Towson University geospatial research & education lab has done something similar. They used Microsoft Image Composite Editor to mosaic pictures captured from a balloon and Microsoft Photosynth for capturing and viewing in 3D.